rs249153

chr12-94930613-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000552205.6(NDUFA12):c.258-2350A>G variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,116 control chromosomes in the GnomAD database, including 4,286 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4286 hom., cov: 32)
• Consequence: NDUFA12 ENST00000552205.6 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.48

Genes affected

NDUFA12 (HGNC:23987): (NADH:ubiquinone oxidoreductase subunit A12) This gene encodes a protein which is part of mitochondrial complex 1, part of the oxidative phosphorylation system in mitochondria. Complex 1 transfers electrons to ubiquinone from NADH which establishes a proton gradient for the generation of ATP. Mutations in this gene are associated with Leigh syndrome due to mitochondrial complex 1 deficiency. Pseudogenes of this gene are located on chromosomes 5 and 13. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFA12	ENST00000552205.6	c.258-2350A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34447 AN: 151994 Hom.: 4278 Cov.: 32

Gnomad AFR AF: 0.321

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0881

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.222

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.227 AC: 34467 AN: 152116 Hom.: 4286 Cov.: 32 AF XY: 0.223 AC XY: 16584 AN XY: 74380

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.0880

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.221

Alfa AF: 0.208 Hom.: 7113

Bravo AF: 0.231

Asia WGS AF: 0.113 AC: 392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.020
Dann	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs249153; hg19: chr12-95324389;